How to manage Handlers in an add-on?
It is simple:

def unregister():
    bpy.app.handlers.scene_update_pre.remove(my_handler)


Blender will call unregister() in the moment you untick the addon in the User Preferences.

my_handler is a function in the global scope of your script, and you append it to the scene update handlers. You can remove it in the same way, by giving a function reference to remove(). It doesn't work if you try to remove a handler callback from outside, because another script hasn't the same function.